Starting phenix.real_space_refine on Wed Mar 20 16:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/03_2024/7lez_23295.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 92 5.16 5 C 17562 2.51 5 N 4710 2.21 5 O 5418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "P PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27794 Number of models: 1 Model: "" Number of chains: 20 Chain: "D" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "G" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.47, per 1000 atoms: 0.52 Number of scatterers: 27794 At special positions: 0 Unit cell: (163.28, 132.08, 153.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 92 16.00 O 5418 8.00 N 4710 7.00 C 17562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 5.5 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 50 sheets defined 26.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.115A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.849A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 285 through 304 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 285 through 304 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.606A pdb=" N HIS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 283' Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 128 Processing helix chain 'P' and resid 183 through 188 Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'M' and resid 23 through 26 Processing helix chain 'M' and resid 27 through 34 Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN M 143 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 207 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 253 through 267 Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU M 282 " --> pdb=" O ASN M 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 283 " --> pdb=" O PRO M 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 279 through 283' Processing helix chain 'M' and resid 285 through 304 Processing helix chain 'N' and resid 23 through 26 Processing helix chain 'N' and resid 27 through 34 Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN N 143 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS N 187 " --> pdb=" O ASP N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 207 Processing helix chain 'N' and resid 207 through 220 Processing helix chain 'N' and resid 253 through 267 Processing helix chain 'N' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU N 282 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY N 283 " --> pdb=" O PRO N 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 279 through 283' Processing helix chain 'N' and resid 285 through 304 Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 267 Processing helix chain 'J' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU J 282 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY J 283 " --> pdb=" O PRO J 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 279 through 283' Processing helix chain 'J' and resid 285 through 304 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS E 134 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 176 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 162 " --> pdb=" O SER E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.707A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER I 176 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER I 162 " --> pdb=" O SER I 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'I' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 94 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 275 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 96 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 174 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR B 50 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE B 10 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 52 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY B 12 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 94 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 275 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE B 174 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 50 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE C 10 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP C 52 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY C 12 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 94 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 275 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE C 174 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER P 176 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER P 162 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'P' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS O 134 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER O 176 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 162 " --> pdb=" O SER O 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 129 through 130 Processing sheet with id=AD2, first strand: chain 'O' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR M 50 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE M 10 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP M 52 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY M 12 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER M 94 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE M 275 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL M 96 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL M 120 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE M 177 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP M 122 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE M 174 " --> pdb=" O LYS M 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR N 50 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE N 10 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP N 52 " --> pdb=" O ILE N 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY N 12 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER N 94 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE N 275 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL N 120 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE N 177 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP N 122 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE N 174 " --> pdb=" O LYS N 196 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR J 50 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE J 10 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP J 52 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY J 12 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER J 94 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE J 275 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL J 96 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL J 120 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 177 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP J 122 " --> pdb=" O ILE J 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE J 174 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.739A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 45 through 50 removed outlier: 6.289A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 69 through 72 removed outlier: 3.866A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS R 207 " --> pdb=" O LYS R 220 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS Q 207 " --> pdb=" O LYS Q 220 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8627 1.34 - 1.46: 4917 1.46 - 1.57: 14736 1.57 - 1.69: 4 1.69 - 1.81: 130 Bond restraints: 28414 Sorted by residual: bond pdb=" CA SER G 77 " pdb=" C SER G 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.81e+01 bond pdb=" CA SER R 77 " pdb=" C SER R 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.79e+01 bond pdb=" CA SER D 77 " pdb=" C SER D 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.78e+01 bond pdb=" CA SER Q 77 " pdb=" C SER Q 77 " ideal model delta sigma weight residual 1.523 1.579 -0.056 1.34e-02 5.57e+03 1.75e+01 bond pdb=" C VAL N 165 " pdb=" N THR N 166 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.61e-02 3.86e+03 7.71e+00 ... (remaining 28409 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.41: 1145 106.41 - 113.36: 15564 113.36 - 120.31: 10321 120.31 - 127.26: 11270 127.26 - 134.21: 356 Bond angle restraints: 38656 Sorted by residual: angle pdb=" CA TYR I 49 " pdb=" CB TYR I 49 " pdb=" CG TYR I 49 " ideal model delta sigma weight residual 113.90 126.47 -12.57 1.80e+00 3.09e-01 4.88e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 126.45 -12.55 1.80e+00 3.09e-01 4.86e+01 angle pdb=" CA TYR O 49 " pdb=" CB TYR O 49 " pdb=" CG TYR O 49 " ideal model delta sigma weight residual 113.90 126.44 -12.54 1.80e+00 3.09e-01 4.85e+01 angle pdb=" CA TYR P 49 " pdb=" CB TYR P 49 " pdb=" CG TYR P 49 " ideal model delta sigma weight residual 113.90 126.41 -12.51 1.80e+00 3.09e-01 4.83e+01 angle pdb=" N ARG P 54 " pdb=" CA ARG P 54 " pdb=" C ARG P 54 " ideal model delta sigma weight residual 110.91 118.47 -7.56 1.17e+00 7.31e-01 4.17e+01 ... (remaining 38651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.78: 15385 12.78 - 25.56: 1261 25.56 - 38.33: 300 38.33 - 51.11: 48 51.11 - 63.89: 24 Dihedral angle restraints: 17018 sinusoidal: 6620 harmonic: 10398 Sorted by residual: dihedral pdb=" CA PRO R 135 " pdb=" C PRO R 135 " pdb=" N LEU R 136 " pdb=" CA LEU R 136 " ideal model delta harmonic sigma weight residual 180.00 123.79 56.21 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO D 135 " pdb=" C PRO D 135 " pdb=" N LEU D 136 " pdb=" CA LEU D 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO G 135 " pdb=" C PRO G 135 " pdb=" N LEU G 136 " pdb=" CA LEU G 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 17015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3317 0.067 - 0.133: 880 0.133 - 0.200: 180 0.200 - 0.267: 17 0.267 - 0.333: 10 Chirality restraints: 4404 Sorted by residual: chirality pdb=" CB ILE M 129 " pdb=" CA ILE M 129 " pdb=" CG1 ILE M 129 " pdb=" CG2 ILE M 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE J 129 " pdb=" CA ILE J 129 " pdb=" CG1 ILE J 129 " pdb=" CG2 ILE J 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE C 129 " pdb=" CA ILE C 129 " pdb=" CG1 ILE C 129 " pdb=" CG2 ILE C 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4401 not shown) Planarity restraints: 4960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO R 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO R 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO R 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO Q 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO Q 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO Q 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.079 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO D 14 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.066 5.00e-02 4.00e+02 ... (remaining 4957 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.98: 16 1.98 - 2.71: 1582 2.71 - 3.44: 40305 3.44 - 4.17: 73692 4.17 - 4.90: 122303 Nonbonded interactions: 237898 Sorted by model distance: nonbonded pdb=" ND1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.255 2.400 nonbonded pdb=" ND1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.255 2.400 nonbonded pdb=" CE1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.368 2.540 nonbonded pdb=" CE1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.368 2.540 nonbonded pdb=" ND1 HIS B 101 " pdb="MN MN B1001 " model vdw 1.437 2.400 ... (remaining 237893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.380 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 71.110 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28414 Z= 0.453 Angle : 1.200 15.475 38656 Z= 0.669 Chirality : 0.064 0.333 4404 Planarity : 0.010 0.121 4960 Dihedral : 10.277 63.891 10350 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.12 % Favored : 89.22 % Rotamer: Outliers : 0.91 % Allowed : 2.60 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 3.48 % Twisted General : 1.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.12), residues: 3618 helix: -2.73 (0.13), residues: 828 sheet: -3.13 (0.15), residues: 914 loop : -2.80 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP Q 111 HIS 0.029 0.005 HIS Q 109 PHE 0.043 0.005 PHE I 118 TYR 0.049 0.004 TYR P 49 ARG 0.012 0.001 ARG O 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 717 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8100 (ptm) cc_final: 0.7549 (ptt) REVERT: D 138 PRO cc_start: 0.1687 (OUTLIER) cc_final: 0.1103 (Cg_exo) REVERT: D 187 TYR cc_start: 0.8593 (m-80) cc_final: 0.8322 (m-80) REVERT: D 205 ILE cc_start: 0.7723 (mt) cc_final: 0.6987 (mm) REVERT: E 117 ILE cc_start: 0.6738 (tt) cc_final: 0.5531 (tt) REVERT: E 181 LEU cc_start: 0.8315 (mt) cc_final: 0.7543 (mp) REVERT: E 195 GLU cc_start: 0.9371 (tt0) cc_final: 0.9105 (tm-30) REVERT: I 93 LEU cc_start: 0.8009 (tm) cc_final: 0.7651 (tt) REVERT: A 95 LEU cc_start: 0.8912 (tp) cc_final: 0.8571 (tp) REVERT: A 172 LYS cc_start: 0.7628 (pttm) cc_final: 0.7104 (tttp) REVERT: A 186 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7457 (mp0) REVERT: B 28 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: B 95 LEU cc_start: 0.8739 (tp) cc_final: 0.8439 (tp) REVERT: B 304 PHE cc_start: 0.7913 (m-80) cc_final: 0.6496 (m-80) REVERT: C 200 MET cc_start: 0.7690 (mmm) cc_final: 0.7444 (mmm) REVERT: C 202 GLU cc_start: 0.7920 (mp0) cc_final: 0.7396 (mp0) REVERT: C 218 TYR cc_start: 0.7603 (t80) cc_final: 0.7224 (t80) REVERT: C 231 PHE cc_start: 0.8460 (t80) cc_final: 0.8106 (t80) REVERT: P 175 MET cc_start: 0.2291 (ttp) cc_final: 0.1680 (ptm) REVERT: P 213 GLU cc_start: 0.6646 (tt0) cc_final: 0.6272 (tt0) REVERT: O 61 ARG cc_start: 0.4663 (ptt-90) cc_final: 0.4089 (ptt90) REVERT: O 94 LEU cc_start: 0.8015 (tt) cc_final: 0.7745 (mt) REVERT: M 66 ILE cc_start: 0.5618 (mm) cc_final: 0.5293 (tt) REVERT: M 111 HIS cc_start: 0.1579 (t-170) cc_final: 0.1230 (t-170) REVERT: M 174 ILE cc_start: 0.6607 (tt) cc_final: 0.6028 (tt) REVERT: M 195 ILE cc_start: 0.4134 (mt) cc_final: 0.3816 (mp) REVERT: M 197 TYR cc_start: 0.6636 (p90) cc_final: 0.5936 (p90) REVERT: M 213 GLU cc_start: 0.8645 (tt0) cc_final: 0.8353 (tm-30) REVERT: M 265 TYR cc_start: 0.6803 (t80) cc_final: 0.6602 (t80) REVERT: M 304 PHE cc_start: 0.2448 (m-80) cc_final: 0.1116 (m-80) REVERT: N 64 PHE cc_start: 0.5465 (t80) cc_final: 0.5203 (t80) REVERT: N 158 ASP cc_start: 0.7680 (m-30) cc_final: 0.7383 (t0) REVERT: N 198 PHE cc_start: 0.6686 (m-80) cc_final: 0.6438 (m-80) REVERT: N 200 MET cc_start: 0.1671 (mmm) cc_final: 0.0565 (mmm) REVERT: N 282 LEU cc_start: 0.1774 (mt) cc_final: 0.1012 (tt) REVERT: J 200 MET cc_start: 0.6658 (mmm) cc_final: 0.6177 (tpp) REVERT: J 262 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6719 (mm-30) REVERT: J 276 MET cc_start: -0.0432 (mmt) cc_final: -0.0761 (mmt) REVERT: G 37 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.6704 (t) REVERT: G 164 LEU cc_start: 0.8714 (mt) cc_final: 0.8435 (tp) REVERT: R 158 PHE cc_start: 0.8701 (t80) cc_final: 0.8391 (t80) REVERT: R 187 TYR cc_start: 0.8306 (m-80) cc_final: 0.7907 (m-80) REVERT: Q 125 SER cc_start: 0.2519 (OUTLIER) cc_final: 0.1791 (p) REVERT: Q 167 ASN cc_start: 0.7307 (m-40) cc_final: 0.7104 (m110) outliers start: 28 outliers final: 4 residues processed: 743 average time/residue: 0.4757 time to fit residues: 515.6956 Evaluate side-chains 346 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 339 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 0.0980 chunk 271 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 280 optimal weight: 30.0000 chunk 108 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 79 GLN A 90 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS C 90 ASN C 115 HIS C 126 HIS C 139 ASN C 143 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 311 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 126 HIS M 141 HIS ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN ** N 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 90 ASN J 141 HIS J 187 HIS J 319 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 109 HIS G 167 ASN R 6 GLN R 55 ASN R 57 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 31 ASN Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 28414 Z= 0.359 Angle : 0.846 11.407 38656 Z= 0.435 Chirality : 0.051 0.227 4404 Planarity : 0.008 0.107 4960 Dihedral : 8.011 63.384 3920 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.76 % Favored : 89.88 % Rotamer: Outliers : 0.29 % Allowed : 3.44 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.13), residues: 3618 helix: -1.19 (0.17), residues: 796 sheet: -2.50 (0.16), residues: 848 loop : -2.34 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G 50 HIS 0.010 0.002 HIS N 187 PHE 0.036 0.003 PHE O 118 TYR 0.036 0.003 TYR O 49 ARG 0.011 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 438 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.7768 (mt0) cc_final: 0.7507 (mm110) REVERT: D 48 MET cc_start: 0.7980 (ptm) cc_final: 0.7653 (ptm) REVERT: D 81 MET cc_start: 0.7897 (ptm) cc_final: 0.7689 (ptm) REVERT: D 93 VAL cc_start: 0.5832 (t) cc_final: 0.5611 (p) REVERT: D 99 GLU cc_start: 0.7483 (tt0) cc_final: 0.6717 (tt0) REVERT: D 150 LEU cc_start: 0.7839 (mt) cc_final: 0.7626 (mp) REVERT: E 49 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4450 (p90) REVERT: E 53 ASN cc_start: 0.8300 (m110) cc_final: 0.8028 (m-40) REVERT: E 136 LEU cc_start: 0.8225 (mp) cc_final: 0.7659 (mp) REVERT: E 145 ASN cc_start: 0.9223 (t0) cc_final: 0.8983 (t0) REVERT: A 172 LYS cc_start: 0.7713 (pttm) cc_final: 0.7485 (ptmm) REVERT: A 186 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7880 (mp0) REVERT: A 206 LEU cc_start: 0.8078 (mt) cc_final: 0.7701 (mt) REVERT: A 212 MET cc_start: 0.7417 (mmm) cc_final: 0.6916 (tpp) REVERT: B 95 LEU cc_start: 0.9142 (tp) cc_final: 0.8885 (tp) REVERT: B 128 ASP cc_start: 0.8853 (m-30) cc_final: 0.8482 (m-30) REVERT: C 77 SER cc_start: 0.9172 (m) cc_final: 0.8865 (p) REVERT: C 202 GLU cc_start: 0.7719 (mp0) cc_final: 0.7099 (mm-30) REVERT: C 205 ARG cc_start: 0.6321 (ttm-80) cc_final: 0.5702 (mtt-85) REVERT: C 276 MET cc_start: 0.8711 (mpp) cc_final: 0.7734 (mtt) REVERT: P 62 PHE cc_start: 0.7320 (m-80) cc_final: 0.7081 (m-80) REVERT: P 105 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6586 (mp0) REVERT: P 175 MET cc_start: 0.1943 (ttp) cc_final: 0.1139 (ttp) REVERT: O 58 ILE cc_start: 0.4038 (tp) cc_final: 0.3819 (tt) REVERT: O 175 MET cc_start: 0.3701 (ptm) cc_final: 0.3234 (tmm) REVERT: O 213 GLU cc_start: 0.8074 (tt0) cc_final: 0.7651 (tm-30) REVERT: M 111 HIS cc_start: 0.2014 (t-170) cc_final: 0.1594 (t-170) REVERT: M 174 ILE cc_start: 0.7045 (tt) cc_final: 0.6731 (tt) REVERT: N 158 ASP cc_start: 0.7719 (m-30) cc_final: 0.7308 (t0) REVERT: N 176 TYR cc_start: 0.4541 (m-80) cc_final: 0.4015 (m-80) REVERT: N 198 PHE cc_start: 0.6625 (m-80) cc_final: 0.5672 (m-80) REVERT: J 262 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6397 (mm-30) REVERT: J 276 MET cc_start: -0.0494 (mmt) cc_final: -0.0966 (mtm) REVERT: G 90 ASP cc_start: 0.6291 (m-30) cc_final: 0.5980 (m-30) REVERT: G 111 TRP cc_start: 0.7679 (p90) cc_final: 0.7352 (p90) REVERT: R 158 PHE cc_start: 0.8792 (t80) cc_final: 0.8204 (t80) REVERT: R 187 TYR cc_start: 0.8244 (m-80) cc_final: 0.7873 (m-80) REVERT: Q 155 LYS cc_start: 0.7627 (mttt) cc_final: 0.7373 (mttt) outliers start: 9 outliers final: 2 residues processed: 446 average time/residue: 0.4542 time to fit residues: 303.5462 Evaluate side-chains 277 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 40.0000 chunk 100 optimal weight: 0.0470 chunk 270 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 325 optimal weight: 30.0000 chunk 351 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN E 157 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 141 HIS A 311 ASN B 79 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 312 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 HIS N 294 ASN ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 28414 Z= 0.358 Angle : 0.818 10.340 38656 Z= 0.420 Chirality : 0.050 0.219 4404 Planarity : 0.007 0.140 4960 Dihedral : 7.467 61.342 3920 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.89 % Favored : 88.72 % Rotamer: Outliers : 0.16 % Allowed : 3.63 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.13), residues: 3618 helix: -0.68 (0.17), residues: 790 sheet: -2.15 (0.16), residues: 850 loop : -2.11 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 122 HIS 0.017 0.003 HIS A 101 PHE 0.040 0.003 PHE I 71 TYR 0.034 0.002 TYR E 49 ARG 0.007 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8157 (mmmm) REVERT: D 48 MET cc_start: 0.8104 (ptm) cc_final: 0.7626 (ptm) REVERT: D 81 MET cc_start: 0.8208 (ptm) cc_final: 0.7517 (ptm) REVERT: D 93 VAL cc_start: 0.5769 (t) cc_final: 0.5481 (p) REVERT: D 150 LEU cc_start: 0.8607 (mt) cc_final: 0.8154 (mp) REVERT: E 117 ILE cc_start: 0.6640 (tt) cc_final: 0.5523 (tt) REVERT: E 145 ASN cc_start: 0.9296 (t0) cc_final: 0.9025 (t0) REVERT: A 130 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7516 (t0) REVERT: A 172 LYS cc_start: 0.7676 (pttm) cc_final: 0.7186 (tttp) REVERT: A 183 ASP cc_start: 0.7641 (m-30) cc_final: 0.6885 (m-30) REVERT: A 186 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7825 (mp0) REVERT: A 212 MET cc_start: 0.7447 (mmm) cc_final: 0.6954 (tpp) REVERT: A 316 ASP cc_start: 0.7169 (t0) cc_final: 0.6832 (t0) REVERT: B 95 LEU cc_start: 0.9003 (tp) cc_final: 0.8623 (tp) REVERT: B 276 MET cc_start: 0.8144 (mmm) cc_final: 0.7016 (mmm) REVERT: B 304 PHE cc_start: 0.7734 (m-80) cc_final: 0.6428 (m-80) REVERT: C 16 SER cc_start: 0.7040 (p) cc_final: 0.6311 (t) REVERT: C 77 SER cc_start: 0.9079 (m) cc_final: 0.8800 (p) REVERT: C 100 ASP cc_start: 0.7539 (p0) cc_final: 0.7240 (p0) REVERT: C 202 GLU cc_start: 0.7597 (mp0) cc_final: 0.7330 (mm-30) REVERT: C 205 ARG cc_start: 0.6381 (ttm-80) cc_final: 0.5653 (mtt-85) REVERT: C 233 VAL cc_start: 0.9565 (m) cc_final: 0.9249 (p) REVERT: P 105 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6565 (mp0) REVERT: P 207 LYS cc_start: 0.8221 (mppt) cc_final: 0.7907 (mppt) REVERT: O 75 ILE cc_start: 0.7116 (mp) cc_final: 0.6737 (mm) REVERT: O 175 MET cc_start: 0.3675 (ptm) cc_final: 0.3201 (tmm) REVERT: O 213 GLU cc_start: 0.7794 (tt0) cc_final: 0.7472 (tm-30) REVERT: M 111 HIS cc_start: 0.1731 (t-170) cc_final: 0.1412 (t-170) REVERT: M 197 TYR cc_start: 0.7186 (p90) cc_final: 0.6940 (p90) REVERT: N 158 ASP cc_start: 0.7684 (m-30) cc_final: 0.7245 (t0) REVERT: N 197 TYR cc_start: 0.7036 (p90) cc_final: 0.6567 (p90) REVERT: J 262 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6387 (mm-30) REVERT: J 265 TYR cc_start: 0.3830 (t80) cc_final: 0.3548 (t80) REVERT: J 276 MET cc_start: -0.0147 (mmt) cc_final: -0.0495 (mtm) REVERT: G 81 MET cc_start: 0.8097 (ppp) cc_final: 0.7821 (ppp) REVERT: R 62 GLN cc_start: 0.7741 (pp30) cc_final: 0.7488 (pp30) REVERT: R 158 PHE cc_start: 0.8778 (t80) cc_final: 0.8262 (t80) REVERT: R 187 TYR cc_start: 0.8405 (m-80) cc_final: 0.8099 (m-80) REVERT: Q 63 LYS cc_start: 0.8311 (pttm) cc_final: 0.7934 (pttm) REVERT: Q 64 LEU cc_start: 0.8528 (mp) cc_final: 0.8274 (pt) REVERT: Q 155 LYS cc_start: 0.7566 (mttt) cc_final: 0.7337 (mttt) outliers start: 5 outliers final: 0 residues processed: 376 average time/residue: 0.4402 time to fit residues: 250.1404 Evaluate side-chains 259 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 326 optimal weight: 30.0000 chunk 346 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 309 optimal weight: 0.0870 chunk 93 optimal weight: 0.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 124 GLN E 212 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 28414 Z= 0.325 Angle : 0.775 10.347 38656 Z= 0.396 Chirality : 0.048 0.201 4404 Planarity : 0.007 0.129 4960 Dihedral : 7.140 57.616 3920 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.39 % Favored : 89.22 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 3618 helix: -0.41 (0.18), residues: 802 sheet: -2.04 (0.16), residues: 938 loop : -1.94 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 163 HIS 0.016 0.002 HIS I 91 PHE 0.031 0.002 PHE I 71 TYR 0.035 0.002 TYR O 49 ARG 0.008 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8146 (ptm) cc_final: 0.7778 (ptm) REVERT: D 93 VAL cc_start: 0.5888 (t) cc_final: 0.5657 (p) REVERT: D 150 LEU cc_start: 0.8652 (mt) cc_final: 0.8133 (mp) REVERT: E 117 ILE cc_start: 0.6924 (tt) cc_final: 0.5614 (tt) REVERT: E 194 CYS cc_start: 0.1396 (p) cc_final: 0.0338 (p) REVERT: A 25 GLU cc_start: 0.7536 (pp20) cc_final: 0.7290 (tm-30) REVERT: A 143 GLN cc_start: 0.8215 (mp10) cc_final: 0.7870 (pm20) REVERT: A 172 LYS cc_start: 0.7695 (pttm) cc_final: 0.7190 (tttp) REVERT: A 183 ASP cc_start: 0.7786 (m-30) cc_final: 0.6801 (m-30) REVERT: A 316 ASP cc_start: 0.7199 (t0) cc_final: 0.6864 (t0) REVERT: B 95 LEU cc_start: 0.9030 (tp) cc_final: 0.8725 (tp) REVERT: B 276 MET cc_start: 0.8133 (mmm) cc_final: 0.7108 (mmm) REVERT: B 304 PHE cc_start: 0.7852 (m-80) cc_final: 0.6370 (m-10) REVERT: C 77 SER cc_start: 0.9071 (m) cc_final: 0.8781 (p) REVERT: C 100 ASP cc_start: 0.7591 (p0) cc_final: 0.7347 (p0) REVERT: P 105 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6461 (mp0) REVERT: O 79 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8551 (tm-30) REVERT: O 81 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8794 (mp0) REVERT: O 175 MET cc_start: 0.3636 (ptm) cc_final: 0.3017 (tmm) REVERT: O 213 GLU cc_start: 0.7817 (tt0) cc_final: 0.7544 (tm-30) REVERT: M 111 HIS cc_start: 0.1751 (t-170) cc_final: 0.1521 (t-170) REVERT: M 174 ILE cc_start: 0.7065 (tt) cc_final: 0.6848 (tt) REVERT: N 158 ASP cc_start: 0.7716 (m-30) cc_final: 0.7243 (t0) REVERT: J 276 MET cc_start: 0.0240 (mmt) cc_final: -0.0316 (mtm) REVERT: R 158 PHE cc_start: 0.8833 (t80) cc_final: 0.8375 (t80) REVERT: R 187 TYR cc_start: 0.8422 (m-80) cc_final: 0.8166 (m-80) REVERT: Q 104 TYR cc_start: -0.0780 (t80) cc_final: -0.1080 (t80) REVERT: Q 123 VAL cc_start: 0.5845 (t) cc_final: 0.5568 (t) REVERT: Q 155 LYS cc_start: 0.7605 (mttt) cc_final: 0.7138 (mtmt) outliers start: 2 outliers final: 0 residues processed: 347 average time/residue: 0.4385 time to fit residues: 232.6360 Evaluate side-chains 247 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 295 optimal weight: 0.8980 chunk 239 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 ASN J 294 ASN ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 28414 Z= 0.311 Angle : 0.757 11.812 38656 Z= 0.387 Chirality : 0.048 0.225 4404 Planarity : 0.007 0.126 4960 Dihedral : 6.885 53.617 3920 Min Nonbonded Distance : 1.196 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.00 % Favored : 88.67 % Rotamer: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 3618 helix: -0.22 (0.18), residues: 802 sheet: -2.00 (0.16), residues: 968 loop : -1.87 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 50 HIS 0.016 0.002 HIS B 101 PHE 0.033 0.002 PHE I 71 TYR 0.032 0.002 TYR O 49 ARG 0.009 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.8120 (ptm) cc_final: 0.7345 (ppp) REVERT: D 93 VAL cc_start: 0.5909 (t) cc_final: 0.5654 (p) REVERT: D 127 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8674 (tmtt) REVERT: D 150 LEU cc_start: 0.8539 (mt) cc_final: 0.8039 (mp) REVERT: D 187 TYR cc_start: 0.8459 (m-80) cc_final: 0.8192 (m-80) REVERT: D 225 ARG cc_start: 0.5280 (pmt-80) cc_final: 0.3785 (ptt-90) REVERT: E 83 PHE cc_start: 0.7943 (m-10) cc_final: 0.7560 (m-80) REVERT: E 117 ILE cc_start: 0.7227 (tt) cc_final: 0.5204 (tt) REVERT: E 145 ASN cc_start: 0.9197 (t0) cc_final: 0.8947 (t0) REVERT: E 183 LYS cc_start: 0.9414 (tttp) cc_final: 0.9184 (tttp) REVERT: E 194 CYS cc_start: 0.2178 (p) cc_final: 0.0520 (p) REVERT: E 207 LYS cc_start: 0.9255 (tmtt) cc_final: 0.9010 (tptp) REVERT: A 172 LYS cc_start: 0.7821 (pttm) cc_final: 0.7329 (tttp) REVERT: A 212 MET cc_start: 0.7382 (mmm) cc_final: 0.7084 (mmm) REVERT: A 316 ASP cc_start: 0.7331 (t0) cc_final: 0.7020 (t0) REVERT: B 95 LEU cc_start: 0.9014 (tp) cc_final: 0.8762 (tp) REVERT: B 274 ASP cc_start: 0.8410 (m-30) cc_final: 0.8101 (m-30) REVERT: B 276 MET cc_start: 0.8189 (mmm) cc_final: 0.7190 (mmm) REVERT: B 304 PHE cc_start: 0.7925 (m-80) cc_final: 0.6597 (m-10) REVERT: C 77 SER cc_start: 0.9037 (m) cc_final: 0.8767 (p) REVERT: C 100 ASP cc_start: 0.7633 (p0) cc_final: 0.7274 (p0) REVERT: C 231 PHE cc_start: 0.8909 (t80) cc_final: 0.8290 (t80) REVERT: C 261 THR cc_start: 0.8896 (p) cc_final: 0.8363 (t) REVERT: P 54 ARG cc_start: 0.6658 (ttm-80) cc_final: 0.6410 (mmm-85) REVERT: P 105 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6854 (mp0) REVERT: P 147 LYS cc_start: 0.9165 (tptt) cc_final: 0.8922 (tptt) REVERT: P 207 LYS cc_start: 0.8218 (mppt) cc_final: 0.7761 (ptpp) REVERT: O 32 TYR cc_start: 0.5780 (m-10) cc_final: 0.5502 (m-80) REVERT: O 175 MET cc_start: 0.3870 (ptm) cc_final: 0.3331 (tmm) REVERT: O 213 GLU cc_start: 0.7892 (tt0) cc_final: 0.7586 (tm-30) REVERT: M 111 HIS cc_start: 0.1763 (t-170) cc_final: 0.1495 (t-170) REVERT: M 197 TYR cc_start: 0.6963 (p90) cc_final: 0.6420 (p90) REVERT: M 308 ARG cc_start: 0.5613 (mmt180) cc_final: 0.5401 (mtt180) REVERT: N 158 ASP cc_start: 0.7707 (m-30) cc_final: 0.7206 (t0) REVERT: N 254 TYR cc_start: 0.5995 (t80) cc_final: 0.5712 (t80) REVERT: J 187 HIS cc_start: 0.6866 (t-170) cc_final: 0.6234 (t-170) REVERT: J 276 MET cc_start: 0.0524 (mmt) cc_final: 0.0058 (mtm) REVERT: G 134 TYR cc_start: 0.8507 (m-80) cc_final: 0.8136 (m-80) REVERT: R 158 PHE cc_start: 0.8861 (t80) cc_final: 0.8380 (t80) REVERT: R 187 TYR cc_start: 0.8439 (m-80) cc_final: 0.8235 (m-80) REVERT: Q 104 TYR cc_start: -0.0457 (t80) cc_final: -0.0697 (t80) REVERT: Q 123 VAL cc_start: 0.5944 (t) cc_final: 0.5651 (t) REVERT: Q 155 LYS cc_start: 0.7636 (mttt) cc_final: 0.7180 (mtmt) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.4281 time to fit residues: 223.2360 Evaluate side-chains 249 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.5980 chunk 311 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 346 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 167 ASN ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 28414 Z= 0.342 Angle : 0.782 10.384 38656 Z= 0.400 Chirality : 0.049 0.253 4404 Planarity : 0.007 0.128 4960 Dihedral : 6.843 48.516 3920 Min Nonbonded Distance : 1.272 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.55 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3618 helix: -0.24 (0.18), residues: 796 sheet: -1.84 (0.17), residues: 930 loop : -1.84 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 200 HIS 0.018 0.002 HIS A 101 PHE 0.033 0.002 PHE G 112 TYR 0.042 0.002 TYR E 49 ARG 0.012 0.001 ARG Q 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8174 (ptm) cc_final: 0.7617 (ptt) REVERT: D 81 MET cc_start: 0.8271 (ptm) cc_final: 0.7696 (ptm) REVERT: D 127 LYS cc_start: 0.8888 (tmmt) cc_final: 0.8603 (tmtt) REVERT: D 150 LEU cc_start: 0.8666 (mt) cc_final: 0.8185 (mp) REVERT: D 187 TYR cc_start: 0.8450 (m-80) cc_final: 0.8139 (m-80) REVERT: D 225 ARG cc_start: 0.5315 (pmt-80) cc_final: 0.4930 (ptp-170) REVERT: E 83 PHE cc_start: 0.7879 (m-80) cc_final: 0.7550 (m-80) REVERT: E 117 ILE cc_start: 0.7257 (tt) cc_final: 0.5941 (tt) REVERT: E 145 ASN cc_start: 0.9180 (t0) cc_final: 0.8967 (t0) REVERT: E 194 CYS cc_start: 0.2305 (p) cc_final: 0.0817 (p) REVERT: A 25 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 172 LYS cc_start: 0.7836 (pttm) cc_final: 0.7359 (tttp) REVERT: A 316 ASP cc_start: 0.7464 (t0) cc_final: 0.7226 (t70) REVERT: B 95 LEU cc_start: 0.9040 (tp) cc_final: 0.8836 (tp) REVERT: B 276 MET cc_start: 0.8176 (mmm) cc_final: 0.7163 (mmm) REVERT: B 304 PHE cc_start: 0.7986 (m-80) cc_final: 0.7022 (m-10) REVERT: C 77 SER cc_start: 0.9057 (m) cc_final: 0.8811 (p) REVERT: C 100 ASP cc_start: 0.7622 (p0) cc_final: 0.7314 (p0) REVERT: C 231 PHE cc_start: 0.8890 (t80) cc_final: 0.8427 (t80) REVERT: C 261 THR cc_start: 0.8962 (p) cc_final: 0.8487 (t) REVERT: C 317 TYR cc_start: 0.6487 (m-80) cc_final: 0.6272 (m-10) REVERT: P 105 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6834 (mp0) REVERT: P 147 LYS cc_start: 0.9169 (tptt) cc_final: 0.8911 (tptt) REVERT: P 149 LYS cc_start: 0.8945 (tptt) cc_final: 0.8521 (tppt) REVERT: O 32 TYR cc_start: 0.5768 (m-80) cc_final: 0.5480 (m-80) REVERT: O 175 MET cc_start: 0.4576 (ptm) cc_final: 0.3691 (tmm) REVERT: M 111 HIS cc_start: 0.1709 (t-170) cc_final: 0.1226 (m-70) REVERT: M 213 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8476 (mt-10) REVERT: M 240 PHE cc_start: 0.6623 (m-80) cc_final: 0.6406 (m-80) REVERT: N 158 ASP cc_start: 0.7743 (m-30) cc_final: 0.7314 (t0) REVERT: N 254 TYR cc_start: 0.5987 (t80) cc_final: 0.5692 (t80) REVERT: J 276 MET cc_start: 0.0930 (mmt) cc_final: 0.0336 (mtm) REVERT: J 279 ASN cc_start: 0.2586 (t0) cc_final: 0.2333 (p0) REVERT: R 158 PHE cc_start: 0.8877 (t80) cc_final: 0.8281 (t80) REVERT: Q 155 LYS cc_start: 0.7653 (mttt) cc_final: 0.7452 (mttt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.4412 time to fit residues: 224.7370 Evaluate side-chains 244 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 195 optimal weight: 40.0000 chunk 291 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN M 126 HIS ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Q 59 ASN Q 62 GLN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.186 28414 Z= 0.484 Angle : 0.908 12.166 38656 Z= 0.463 Chirality : 0.053 0.286 4404 Planarity : 0.007 0.142 4960 Dihedral : 7.116 45.732 3920 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.77 % Favored : 86.90 % Rotamer: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.14), residues: 3618 helix: -0.74 (0.17), residues: 838 sheet: -1.89 (0.16), residues: 966 loop : -2.16 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 163 HIS 0.022 0.003 HIS C 111 PHE 0.044 0.003 PHE I 71 TYR 0.027 0.003 TYR O 49 ARG 0.012 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8113 (mmmm) REVERT: D 48 MET cc_start: 0.8175 (ptm) cc_final: 0.7913 (ptm) REVERT: D 127 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8500 (tmtt) REVERT: D 150 LEU cc_start: 0.8745 (mt) cc_final: 0.8282 (mp) REVERT: D 187 TYR cc_start: 0.8554 (m-80) cc_final: 0.8153 (m-80) REVERT: E 83 PHE cc_start: 0.7827 (m-80) cc_final: 0.7598 (m-80) REVERT: E 117 ILE cc_start: 0.7449 (tt) cc_final: 0.5970 (tt) REVERT: E 145 ASN cc_start: 0.9191 (t0) cc_final: 0.8962 (t0) REVERT: E 194 CYS cc_start: 0.2836 (p) cc_final: 0.0783 (p) REVERT: A 42 GLU cc_start: 0.8076 (mp0) cc_final: 0.7512 (mp0) REVERT: A 172 LYS cc_start: 0.7971 (pttm) cc_final: 0.7469 (tttp) REVERT: B 276 MET cc_start: 0.8222 (mmm) cc_final: 0.7215 (mmm) REVERT: C 261 THR cc_start: 0.9056 (p) cc_final: 0.8641 (t) REVERT: P 62 PHE cc_start: 0.7656 (m-80) cc_final: 0.7429 (m-80) REVERT: P 105 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6826 (mp0) REVERT: P 149 LYS cc_start: 0.9030 (tptt) cc_final: 0.8628 (mmmm) REVERT: O 175 MET cc_start: 0.4565 (ptm) cc_final: 0.3595 (tmm) REVERT: M 111 HIS cc_start: 0.2637 (t-170) cc_final: 0.1799 (m-70) REVERT: M 214 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8415 (mt-10) REVERT: M 274 ASP cc_start: 0.2720 (m-30) cc_final: 0.2507 (m-30) REVERT: N 158 ASP cc_start: 0.7672 (m-30) cc_final: 0.7139 (t0) REVERT: N 198 PHE cc_start: 0.6496 (m-80) cc_final: 0.5919 (m-80) REVERT: J 187 HIS cc_start: 0.7355 (t-170) cc_final: 0.7087 (t-90) REVERT: J 276 MET cc_start: 0.1199 (mmt) cc_final: 0.0324 (mtm) REVERT: J 279 ASN cc_start: 0.2801 (t0) cc_final: 0.2505 (p0) REVERT: G 81 MET cc_start: 0.8193 (ppp) cc_final: 0.7935 (ppp) REVERT: R 158 PHE cc_start: 0.8939 (t80) cc_final: 0.8343 (t80) REVERT: R 187 TYR cc_start: 0.8545 (m-80) cc_final: 0.8295 (m-80) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.4304 time to fit residues: 213.6322 Evaluate side-chains 229 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 chunk 206 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 235 optimal weight: 30.0000 chunk 170 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 271 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 212 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 126 HIS ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Q 109 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28414 Z= 0.220 Angle : 0.737 10.440 38656 Z= 0.374 Chirality : 0.048 0.194 4404 Planarity : 0.007 0.120 4960 Dihedral : 6.652 46.634 3920 Min Nonbonded Distance : 1.369 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.45 % Favored : 89.28 % Rotamer: Outliers : 0.10 % Allowed : 1.07 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3618 helix: 0.09 (0.18), residues: 802 sheet: -1.75 (0.17), residues: 968 loop : -1.87 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 163 HIS 0.010 0.001 HIS B 101 PHE 0.040 0.002 PHE G 112 TYR 0.042 0.002 TYR E 49 ARG 0.008 0.001 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 313 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8051 (mmmm) REVERT: D 48 MET cc_start: 0.8184 (ptm) cc_final: 0.7818 (ptt) REVERT: D 81 MET cc_start: 0.7139 (ppp) cc_final: 0.5891 (ppp) REVERT: D 127 LYS cc_start: 0.8913 (tmmt) cc_final: 0.8599 (tmtt) REVERT: D 187 TYR cc_start: 0.8476 (m-80) cc_final: 0.8061 (m-80) REVERT: E 83 PHE cc_start: 0.7757 (m-80) cc_final: 0.7495 (m-80) REVERT: E 117 ILE cc_start: 0.7300 (tt) cc_final: 0.6122 (tt) REVERT: E 145 ASN cc_start: 0.9186 (t0) cc_final: 0.8969 (t0) REVERT: E 194 CYS cc_start: 0.2757 (p) cc_final: 0.0416 (p) REVERT: I 3 VAL cc_start: 0.8769 (m) cc_final: 0.8406 (p) REVERT: A 55 PHE cc_start: 0.6417 (m-10) cc_final: 0.6056 (m-10) REVERT: A 172 LYS cc_start: 0.7687 (pttm) cc_final: 0.7223 (tttp) REVERT: A 254 TYR cc_start: 0.8613 (t80) cc_final: 0.8079 (t80) REVERT: B 212 MET cc_start: 0.8517 (mmm) cc_final: 0.8293 (mtp) REVERT: B 276 MET cc_start: 0.8224 (mmm) cc_final: 0.7363 (mmm) REVERT: B 304 PHE cc_start: 0.7673 (m-80) cc_final: 0.6857 (m-10) REVERT: P 62 PHE cc_start: 0.7769 (m-80) cc_final: 0.7469 (m-80) REVERT: P 105 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6815 (mp0) REVERT: P 154 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7413 (mm-30) REVERT: P 175 MET cc_start: 0.3960 (tmm) cc_final: 0.3652 (tmm) REVERT: O 32 TYR cc_start: 0.6578 (m-80) cc_final: 0.6092 (m-10) REVERT: O 175 MET cc_start: 0.4652 (ptm) cc_final: 0.3999 (tmm) REVERT: M 60 ASN cc_start: 0.7806 (t0) cc_final: 0.7485 (m110) REVERT: M 111 HIS cc_start: 0.2322 (t-170) cc_final: 0.1860 (m90) REVERT: M 213 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8467 (mm-30) REVERT: N 158 ASP cc_start: 0.7738 (m-30) cc_final: 0.7279 (t0) REVERT: N 198 PHE cc_start: 0.6381 (m-80) cc_final: 0.5788 (m-80) REVERT: N 200 MET cc_start: 0.0810 (mtm) cc_final: 0.0426 (ptp) REVERT: N 254 TYR cc_start: 0.6039 (t80) cc_final: 0.5792 (t80) REVERT: J 200 MET cc_start: 0.6365 (mmt) cc_final: 0.5663 (mmt) REVERT: J 276 MET cc_start: 0.1054 (mmt) cc_final: 0.0316 (mtm) REVERT: G 111 TRP cc_start: 0.7732 (p90) cc_final: 0.7111 (p90) REVERT: R 158 PHE cc_start: 0.8718 (t80) cc_final: 0.8218 (t80) REVERT: R 187 TYR cc_start: 0.8491 (m-80) cc_final: 0.8187 (m-80) REVERT: Q 46 GLU cc_start: 0.5618 (tm-30) cc_final: 0.5133 (tm-30) outliers start: 3 outliers final: 0 residues processed: 316 average time/residue: 0.4284 time to fit residues: 208.5814 Evaluate side-chains 225 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.9990 chunk 330 optimal weight: 30.0000 chunk 301 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 304 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28414 Z= 0.233 Angle : 0.733 9.694 38656 Z= 0.371 Chirality : 0.048 0.233 4404 Planarity : 0.006 0.118 4960 Dihedral : 6.513 43.820 3920 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.14 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3618 helix: 0.24 (0.19), residues: 796 sheet: -1.68 (0.17), residues: 956 loop : -1.80 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 163 HIS 0.014 0.002 HIS J 187 PHE 0.033 0.002 PHE G 112 TYR 0.039 0.002 TYR P 49 ARG 0.006 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8134 (ptm) cc_final: 0.7794 (ptt) REVERT: D 81 MET cc_start: 0.7233 (ppp) cc_final: 0.6086 (ppp) REVERT: D 127 LYS cc_start: 0.8908 (tmmt) cc_final: 0.8667 (tmtt) REVERT: D 150 LEU cc_start: 0.8354 (mt) cc_final: 0.7822 (mp) REVERT: D 187 TYR cc_start: 0.8352 (m-80) cc_final: 0.7977 (m-80) REVERT: E 35 TRP cc_start: 0.8418 (m100) cc_final: 0.7634 (m100) REVERT: E 79 GLU cc_start: 0.8106 (tp30) cc_final: 0.7834 (tm-30) REVERT: E 145 ASN cc_start: 0.9199 (t0) cc_final: 0.8996 (t0) REVERT: E 194 CYS cc_start: 0.4362 (p) cc_final: 0.3123 (p) REVERT: I 3 VAL cc_start: 0.8743 (m) cc_final: 0.8468 (p) REVERT: A 55 PHE cc_start: 0.6347 (m-10) cc_final: 0.6068 (m-10) REVERT: A 172 LYS cc_start: 0.7711 (pttm) cc_final: 0.7237 (tttp) REVERT: A 254 TYR cc_start: 0.8449 (t80) cc_final: 0.8164 (t80) REVERT: B 274 ASP cc_start: 0.8503 (m-30) cc_final: 0.8302 (m-30) REVERT: B 276 MET cc_start: 0.8214 (mmm) cc_final: 0.7291 (mmm) REVERT: B 304 PHE cc_start: 0.7706 (m-80) cc_final: 0.7035 (m-10) REVERT: P 62 PHE cc_start: 0.7835 (m-80) cc_final: 0.7484 (m-80) REVERT: P 105 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6851 (mp0) REVERT: P 149 LYS cc_start: 0.8903 (tptt) cc_final: 0.8676 (mmmm) REVERT: P 175 MET cc_start: 0.3958 (tmm) cc_final: 0.3603 (tmm) REVERT: O 32 TYR cc_start: 0.6561 (m-80) cc_final: 0.6107 (m-10) REVERT: O 175 MET cc_start: 0.4453 (ptm) cc_final: 0.3679 (tmm) REVERT: M 60 ASN cc_start: 0.7763 (t0) cc_final: 0.7439 (m110) REVERT: N 158 ASP cc_start: 0.7807 (m-30) cc_final: 0.7371 (t0) REVERT: N 198 PHE cc_start: 0.6793 (m-80) cc_final: 0.6223 (m-80) REVERT: N 200 MET cc_start: 0.0942 (mtm) cc_final: 0.0652 (ptp) REVERT: N 254 TYR cc_start: 0.6085 (t80) cc_final: 0.5822 (t80) REVERT: J 200 MET cc_start: 0.6355 (mmt) cc_final: 0.5637 (mmt) REVERT: J 276 MET cc_start: 0.1382 (mmt) cc_final: 0.0772 (mtm) REVERT: G 13 LYS cc_start: 0.9255 (pttp) cc_final: 0.8760 (mmmm) REVERT: G 111 TRP cc_start: 0.7643 (p90) cc_final: 0.7082 (p90) REVERT: G 199 THR cc_start: 0.8715 (p) cc_final: 0.8393 (p) REVERT: R 158 PHE cc_start: 0.8694 (t80) cc_final: 0.8195 (t80) REVERT: R 187 TYR cc_start: 0.8520 (m-80) cc_final: 0.8206 (m-80) REVERT: Q 46 GLU cc_start: 0.5734 (tm-30) cc_final: 0.5311 (tm-30) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.4280 time to fit residues: 194.6234 Evaluate side-chains 231 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 236 optimal weight: 0.0370 chunk 356 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 219 optimal weight: 0.3980 chunk 174 optimal weight: 8.9990 overall best weight: 2.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 28414 Z= 0.317 Angle : 0.775 10.887 38656 Z= 0.395 Chirality : 0.050 0.309 4404 Planarity : 0.007 0.122 4960 Dihedral : 6.556 44.365 3920 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.89 % Favored : 87.89 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3618 helix: 0.23 (0.19), residues: 784 sheet: -1.60 (0.17), residues: 942 loop : -1.76 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 200 HIS 0.013 0.002 HIS J 187 PHE 0.034 0.002 PHE G 112 TYR 0.038 0.002 TYR E 49 ARG 0.009 0.001 ARG D 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8279 (ptm) cc_final: 0.7928 (ptt) REVERT: D 81 MET cc_start: 0.7434 (ppp) cc_final: 0.6287 (ppp) REVERT: D 119 THR cc_start: 0.8051 (p) cc_final: 0.7788 (p) REVERT: D 127 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8662 (tmtt) REVERT: D 150 LEU cc_start: 0.8409 (mt) cc_final: 0.7915 (mp) REVERT: D 187 TYR cc_start: 0.8395 (m-80) cc_final: 0.8047 (m-80) REVERT: E 79 GLU cc_start: 0.8105 (tp30) cc_final: 0.7795 (tm-30) REVERT: E 83 PHE cc_start: 0.7857 (m-10) cc_final: 0.7531 (m-80) REVERT: E 145 ASN cc_start: 0.9145 (t0) cc_final: 0.8921 (t0) REVERT: A 55 PHE cc_start: 0.6264 (m-10) cc_final: 0.5960 (m-10) REVERT: A 172 LYS cc_start: 0.7774 (pttm) cc_final: 0.7319 (tttp) REVERT: A 295 THR cc_start: 0.5483 (m) cc_final: 0.5240 (p) REVERT: B 212 MET cc_start: 0.8629 (mmm) cc_final: 0.8213 (mtp) REVERT: B 274 ASP cc_start: 0.8650 (m-30) cc_final: 0.8431 (m-30) REVERT: B 276 MET cc_start: 0.8255 (mmm) cc_final: 0.7333 (mmm) REVERT: B 304 PHE cc_start: 0.7919 (m-80) cc_final: 0.7425 (m-10) REVERT: C 200 MET cc_start: 0.9106 (mmt) cc_final: 0.8754 (mmm) REVERT: C 261 THR cc_start: 0.8935 (p) cc_final: 0.8388 (t) REVERT: P 62 PHE cc_start: 0.7865 (m-80) cc_final: 0.7507 (m-80) REVERT: P 105 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6875 (mp0) REVERT: P 149 LYS cc_start: 0.8938 (tptt) cc_final: 0.8706 (mmmm) REVERT: P 175 MET cc_start: 0.4218 (tmm) cc_final: 0.3831 (tmm) REVERT: O 32 TYR cc_start: 0.6533 (m-80) cc_final: 0.6094 (m-80) REVERT: O 175 MET cc_start: 0.4706 (ptm) cc_final: 0.3967 (tmm) REVERT: M 111 HIS cc_start: 0.2560 (t-170) cc_final: 0.1804 (m90) REVERT: M 308 ARG cc_start: 0.5330 (mtt180) cc_final: 0.4746 (mtp180) REVERT: N 158 ASP cc_start: 0.7828 (m-30) cc_final: 0.7384 (t0) REVERT: N 198 PHE cc_start: 0.6566 (m-80) cc_final: 0.6032 (m-80) REVERT: N 200 MET cc_start: 0.1181 (mtm) cc_final: 0.0931 (ptp) REVERT: N 254 TYR cc_start: 0.6079 (t80) cc_final: 0.5869 (t80) REVERT: J 200 MET cc_start: 0.6489 (mmt) cc_final: 0.5775 (mmt) REVERT: J 276 MET cc_start: 0.1830 (mmt) cc_final: 0.1186 (mtm) REVERT: G 13 LYS cc_start: 0.9289 (pttp) cc_final: 0.8987 (mmmt) REVERT: G 199 THR cc_start: 0.8731 (p) cc_final: 0.8390 (p) REVERT: R 158 PHE cc_start: 0.8794 (t80) cc_final: 0.8241 (t80) REVERT: R 187 TYR cc_start: 0.8556 (m-80) cc_final: 0.8241 (m-80) REVERT: Q 46 GLU cc_start: 0.5805 (tm-30) cc_final: 0.5408 (tm-30) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.4272 time to fit residues: 183.1029 Evaluate side-chains 208 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 5.9990 chunk 302 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.123938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.094583 restraints weight = 112294.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.091563 restraints weight = 103741.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.091508 restraints weight = 84385.790| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28414 Z= 0.211 Angle : 0.723 9.857 38656 Z= 0.366 Chirality : 0.048 0.217 4404 Planarity : 0.006 0.121 4960 Dihedral : 6.385 43.872 3920 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.53 % Favored : 89.33 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3618 helix: 0.35 (0.19), residues: 796 sheet: -1.47 (0.17), residues: 926 loop : -1.73 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 200 HIS 0.013 0.001 HIS J 187 PHE 0.029 0.002 PHE M 304 TYR 0.034 0.002 TYR E 49 ARG 0.017 0.001 ARG M 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5704.29 seconds wall clock time: 105 minutes 35.22 seconds (6335.22 seconds total)